We've upgraded to 1.6.1 since this report. The problems we've encountered during the upgrade suggest there may be something wrong in earlier ATutors (1.4.3+) and/or our configurations back then that might have caused the bug.
Unlike most people, we used UTF-8 on our production site from the beginning, which might explain why no-one reports a similar bug.

Currently I don't have time to investigate it, so let's assume it's our unique problem and close this issue.
I'll reopen it when/if I have time to find the cause.